Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae
Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D1D1XcrXcr and 2n = 6x = 42, D1D1XcrXcrD2D2, respectively) that are similar morphological...
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.980764/full |
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| author | Pavel Yu. Kroupin Ekaterina D. Badaeva Ekaterina D. Badaeva Victoria M. Sokolova Nadezhda N. Chikida Maria Kh. Belousova Sergei A. Surzhikov Ekaterina A. Nikitina Alina A. Kocheshkova Daniil S. Ulyanov Aleksey S. Ermolaev Thi Mai Luong Khuat Olga V. Razumova Anna I. Yurkina Gennady I. Karlov Mikhail G. Divashuk |
| author_facet | Pavel Yu. Kroupin Ekaterina D. Badaeva Ekaterina D. Badaeva Victoria M. Sokolova Nadezhda N. Chikida Maria Kh. Belousova Sergei A. Surzhikov Ekaterina A. Nikitina Alina A. Kocheshkova Daniil S. Ulyanov Aleksey S. Ermolaev Thi Mai Luong Khuat Olga V. Razumova Anna I. Yurkina Gennady I. Karlov Mikhail G. Divashuk |
| author_sort | Pavel Yu. Kroupin |
| collection | DOAJ |
| description | Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D1D1XcrXcr and 2n = 6x = 42, D1D1XcrXcrD2D2, respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D1 and D2 subgenomes of Ae. crassa were contributed by Aegilopstauschii (2n = 2x = 14, DD), while the Xcr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (Jb genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D1 or Xcr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species. |
| first_indexed | 2024-03-13T00:05:57Z |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-13T00:05:57Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-92edfbe485f24c2e8560b11d48fabefe2023-07-13T03:39:58ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-10-011310.3389/fpls.2022.980764980764Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the TriticeaePavel Yu. Kroupin0Ekaterina D. Badaeva1Ekaterina D. Badaeva2Victoria M. Sokolova3Nadezhda N. Chikida4Maria Kh. Belousova5Sergei A. Surzhikov6Ekaterina A. Nikitina7Alina A. Kocheshkova8Daniil S. Ulyanov9Aleksey S. Ermolaev10Thi Mai Luong Khuat11Olga V. Razumova12Anna I. Yurkina13Gennady I. Karlov14Mikhail G. Divashuk15All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, RussiaN.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, RussiaAll-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, RussiaAll-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, RussiaAgricultural Genetics Institute, Department of Molecular Biology, Hanoi, VietnamAll-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, RussiaAegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D1D1XcrXcr and 2n = 6x = 42, D1D1XcrXcrD2D2, respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D1 and D2 subgenomes of Ae. crassa were contributed by Aegilopstauschii (2n = 2x = 14, DD), while the Xcr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (Jb genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D1 or Xcr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.https://www.frontiersin.org/articles/10.3389/fpls.2022.980764/fullAegilopsshallow whole-genome sequencingfluorescence in situ hybridizationchromosomessatellite repeatsrepeatome |
| spellingShingle | Pavel Yu. Kroupin Ekaterina D. Badaeva Ekaterina D. Badaeva Victoria M. Sokolova Nadezhda N. Chikida Maria Kh. Belousova Sergei A. Surzhikov Ekaterina A. Nikitina Alina A. Kocheshkova Daniil S. Ulyanov Aleksey S. Ermolaev Thi Mai Luong Khuat Olga V. Razumova Anna I. Yurkina Gennady I. Karlov Mikhail G. Divashuk Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae Frontiers in Plant Science Aegilops shallow whole-genome sequencing fluorescence in situ hybridization chromosomes satellite repeats repeatome |
| title | Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae |
| title_full | Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae |
| title_fullStr | Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae |
| title_full_unstemmed | Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae |
| title_short | Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae |
| title_sort | aegilops crassa boiss repeatome characterized using low coverage ngs as a source of new fish markers application in phylogenetic studies of the triticeae |
| topic | Aegilops shallow whole-genome sequencing fluorescence in situ hybridization chromosomes satellite repeats repeatome |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.980764/full |
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